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Abstract Background Accurately identifying effective biomarkers and translating them into clinical practice have significant implications for improving clinical outcomes in hepatocellular carcinoma (HCC). In this study, our objective is to explore appropriate methods to improve the accuracy of biomarker identification and investigate their clinical value. Methods Concentrating on the N6-methyladenosine (m6A) modification regulators, we utilized dozens of multi-omics HCC datasets to analyze the expression patterns and genetic features of m6A regulators. Through the integration of big data analysis with function experiments, we have redefined the biological roles of m6A regulators in HCC. Based on the key regulators, we constructed m6A risk models and explored their clinical value in estimating prognosis and guiding personalized therapy for HCC. Results Most m6A regulators exhibit abnormal expression in HCC, and their expression is influenced by copy number variations (CNV) and DNA methylation. Large-scale data analysis has revealed the biological roles of many key m6A regulators, and these findings are well consistent with experimental results. The m6A risk models offer significant prognostic value. Moreover, they assist in reassessing the therapeutic potential of drugs such as sorafenib, gemcitabine, CTLA4 and PD1 blockers in HCC. Conclusions Our findings suggest that the mutual validation of big data analysis and functional experiments may facilitate the precise identification and definition of biomarkers, and our m6A risk models may have the potential to guide personalized chemotherapy, targeted treatment, and immunotherapy decisions in HCC.

In previous study we characterized the oncogenic role of long non-coding RNA MALAT1 in esophageal squamous cell carcinoma (ESCC), but the detailed mechanism remains obscure. Here we identified glyoxalase 1 (GLO1) as the most possible executor of MALAT1 by microarray screening. GLO1 is responsible for degradation of cytotoxic methylglyoxal (MGO), which is by-product of tumor glycolysis. Accumulated MGO may lead to glycation of DNA and protein, resulting in elevated advanced glycation end products (AGEs), while glyoxalase 1 detoxify MGO to alleviate its cytotoxic effect to tumor cells. GLO1 interfering led to accumulation of AGEs and following activation of DNA injury biomarkers, which lead to cell cycle arrest and growth inhibition. In silico analysis based on online database revealed abundant enrichment of histone acetylation marker H3K27ac in GLO1 promotor, and acetyltransferase inhibitor C646 declined GLO1 expression. Acetyltransferase KAT2B, which was also identified as a target of MALAT, mediated histone lysine acetylation of GLO1 promotor, which was confirmed by ChIP-qPCR experiment. Shared binding sites of miR-206 were found on MALAT1 and KAT2B mRNA. Dual-luciferase reporter assays confirmed interaction within MALAT1-miR-206-GLO1. Finally, we identified MALAT1 encapsuled by exosome from donor cells, and transferred malignant behaviors to recipient cells. The secreted exosomes may enter circulation, and serum MALAT1 level combined with traditional tumor markers showed potential power for ESCC diagnosis.

Abstract Background DNMT3L is a crucial DNA methylation regulatory factor, yet its function and mechanism in hepatocellular carcinoma (HCC) remain poorly understood. Bioinformatics-based big data analysis has increasingly gained significance in cancer research. Therefore, this study aims to elucidate the role of DNMT3L in HCC by integrating big data analysis with experimental validation. Methods Dozens of HCC datasets were collected to analyze the expression of DNMT3L and its relationship with prognostic indicators, and were used for molecular regulatory relationship evaluation. The effects of DNMT3L on the malignant phenotypes of hepatoma cells were confirmed in vitro and in vivo. The regulatory mechanisms of DNMT3L were explored through MSP, western blot, and dual-luciferase assays. Results DNMT3L was found to be downregulated in HCC tissues and associated with better prognosis. Overexpression of DNMT3L inhibits cell proliferation and metastasis. Additionally, CDO1 was identified as a target gene of DNMT3L and also exhibits anti-cancer effects. DNMT3L upregulates CDO1 expression by competitively inhibiting DNMT3A-mediated methylation of CDO1 promoter. Conclusions Our study revealed the role and epi-transcriptomic regulatory mechanism of DNMT3L in HCC, and underscored the essential role and applicability of big data analysis in elucidating complex biological processes.

In this paper, the boundary layer and entropy production characteristics of a Casson nanofluid moving nonlinearly in a wedge-shaped stretching plate under an unsteady flow are investigated. In the course of the study, the continuity, momentum, energy and concentration equations are changed into nonlinear ordinary differential equations by similarity transformation, and numerical solution methods are used to obtain the effects of several dimensionless parameters on velocity, temperature, concentration and entropy production. The results show that changes in the magnetic field, buoyancy and Casson parameters lead to changes in the fluid viscosity, which in turn affects the thermal mass-transfer properties of the fluid. It is also found that the Brinkman number is proportional to the entropy production and inversely proportional to the Bejan number. The results of Casson nanofluid heat and mass transfer and entropy production can provide important theoretical support for applications in the field of Casson fluid engineering.

Abstract Background Exosomal long non‐coding RNA (lncRNA) has been shown to be potential biomarker for cancer diagnosis and follow up. However, little is known about its application in esophageal squamous cell carcinoma (ESCC) detection. Here, we sought to develop a novel diagnostic model based on serum exosomal lncRNAs to improve ESCC screening efficiency. Methods A multiphase, case‐control study was conducted among 140 ESCC patients and 140 healthy controls. Microarray screening was performed to acquire differentially expressed exosomal lncRNAs in the discovery phase. The diagnostic model Index I was constructed based on a panel of three lncRNAs using logistic regression in the training phase, and were confirmed in a subsequent validation phase. A receiver operating characteristic (ROC) curve was generated to calculate the diagnostic value. The effects of the selected lncRNAs level on ESCC mortality were evaluated using a Cox hazard regression model and Kaplan‐Meier curve analysis, and the expression level with clinicopathological features was also calculated. Finally, we explored the oncogenic potential of candidate lncRNA RASSF8‐AS1 in vitro and by target mRNA sequencing. Results Index I was able to discriminate ESCC patients from healthy controls, and showed superiority to classic tumor biomarkers. Moreover, serum levels of the exosomal lncRNAs correlated with clinicopathological features and prognosis. The in vitro assays showed that RASSF8‐AS1 played an oncogenic role in ESCC. Target mRNA scanning results suggested involvement of RASSF8‐AS1 in tumor immunity and metabolism. Conclusion The newly identified serum exosomal lncRNAs could be used as new biomarkers for ESCC, and showed oncogenic potential in ESCC.

Abstract Ferroptosis is a novel type of cell death depending on iron and is strongly related to the development of tumors. Hepatocellular carcinoma (HCC) is a malignancy with high incidence. Despite some reports demonstrating the relation between ferroptosis-related genes and HCC, more details have not been excavated. In the present study, we collected and analyzed HCC patients' datasets from the TCGA-LIHC project and ICGC portal, respectively. Through the bioinformatic methods, we screened 126 differentially expressed genes. Then a prognostic model was established with four genes (GPX2, MT3, PRDX1, and SRXN1). PRDX1 is the hub gene of the prognosis model and has a high expression in hepatocellular carcinoma tumor tissue and cell lines. We further found that silencing PRDX1 increased the accumulation of ferrous ions and lipid peroxidation accumulation in HEPG2 cells and promoted ferroptosis in hepatocellular carcinoma. In conclusion, the study demonstrated the four-gene signature can be used to predict HCC prognosis. It also revealed the potential function of the ferroptosis-related gene PRDX1 in HCC, which can be a biomarker of the prediction for HCC outcome.

The highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) often causes secondary bacterial infection in piglets, resulting in inflammatory lung injury and leading to high mortality rates and significant economic losses in the pig industry. Microvascular endothelial cells (MVECs) play a crucial role in the inflammatory response. Previous studies have shown that HP-PRRSV can infect porcine pulmonary MVECs and damage the endothelial glycocalyx. To further understand the role of pulmonary MVECs in the pathogenesis of HP-PRRSV and its secondary bacterial infection, in this study, cultured porcine pulmonary MVECs were stimulated with a HP-PRRSV HN strain and lipopolysaccharide (LPS). The changes in gene expression profiles were analyzed through transcriptome sequencing, and the differentially expressed genes were verified using qRT-PCR, Western blot, and ELISA. Furthermore, the effects on endothelial barrier function and regulation of neutrophil trans-endothelial migration were detected using the Transwell model. HP-PRRSV primarily induced differential expression of numerous genes associated with immune response, including IFIT2, IFIT3, VCAM1, ITGB4, and CCL5, whereas LPS triggered an inflammatory response involving IL6, IL16, CXCL8, CXCL14, and ITGA7. Compared to the individual effect of LPS, when given after HN-induced stimulation, it caused a greater number of changes in inflammatory molecules, such as VCAM1, IL1A, IL6, IL16, IL17D, CCL5, ITGAV, IGTB8, and TNFAIP3A, a more significant reduction in transendothelial electrical resistance, and higher increase in neutrophil transendothelial migration. In summary, these results suggest a synergistic effect of HP-PRRSV and LPS on the inflammatory response of porcine pulmonary MVECs. This study provides insights into the mechanism of severe lung injury caused by secondary bacterial infection following HP-PRRSV infection from the perspective of MVECs, emphasizing the vital role of pulmonary MVECs in HP-PRRSV infection.

Acoustic emission (AE) testing and Lamb wave inspection techniques have been widely used in non-destructive testing and structural health monitoring. For thin plates, the AEs arising from structural defect development (e.g., fatigue crack propagation) propagate as Lamb waves, and Lamb wave modes can be used to provide important information about the growth and localisation of defects. However, few sensors can be used to achieve the in situ wavenumber–frequency modal decomposition of AEs. This study explores the ability of a new multi-element piezoelectric sensor array to decompose AEs excited by pencil lead breaks (PLBs) on a thin isotropic plate. In this study, AEs were generated by out-of-plane (transverse) and in-plane (longitudinal) PLBs applied at the edge of the plate, and waveforms were recorded by both the new sensor array and a commercial AE sensor. Finite element analysis (FEA) simulations of PLBs were also conducted and the results were compared with the experimental results. To identify the wave modes present, the longitudinal and transverse PLB test results recorded by the new sensor array at five different plate locations were compared with FEA simulations using the same arrangement. Two-dimensional fast Fourier Transforms were then applied to the AE wavefields. It was found that the AE modal composition was dependent on the orientation of the PLB direction. The results suggest that this new sensor array can be used to identify the AE wave modes excited by PLBs in both in-plane and out-of-plane directions.

BackgroundFerroptosis is a new type of cell death different from apoptosis, necrosis, autophagy, and pyroptosis. This study aimed to explore the relationship between ferroptosis-related noncoding RNA (ncRNA) and gastric adenocarcinoma with regard to immunity and prognosis.MethodsFerroptosis-related ncRNA expression profiles and clinical pathology and overall survival information were collected from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus database. The ferroptosis-related ncRNA signature was identified by Cox regression analysis and the least absolute shrinkage and selection operator analysis. The survival analysis, receiver operating characteristic (ROC) analysis, and decision curve analysis were adopted to evaluate the prognostic prediction performance of the signature. The correlation between risk and multiple clinical characteristics was analyzed using the chi-square test. The Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and gene set enrichment analysis were used for mining functions and pathways. The CIBERSORT, ssGSEA, and ESTIMATE algorithms were used to assess immune infiltration and the tumor microenvironment. The response of immunotherapy was predicted using the Submap algorithm, and the Connectivity Map and the ridge regression model were used to screen and evaluate drugs.ResultsA carcinogenic risk signature was constructed using five ferroptosis-related ncRNAs. It showed an extraordinary ability to predict the prognoses of patients with gastric adenocarcinoma [area under the ROC curve (AUC) after 6 years = 0.689; GSE84426, AUC after 6 years = 0.747]. The lower ferroptosis potential level and lower tumor mutation burden were related to the poor prognoses of patients. The high-risk group had more immune cell recruitment, and the overall effect of the anti-immune checkpoint immunotherapy was not as good as that of the low-risk group. The high- and low-risk groups were enriched in tumor- and immune-related pathways, respectively. The screened antitumor drugs, such as genistein, guanabenz, and betulinic acid, improved the survival of the patients.ConclusionsThe ferroptosis-related ncRNA signature is a potential carcinogenic prognostic biomarker of gastric adenocarcinoma.

While acoustic emission (AE) testing can be used as a valuable technique in structural health monitoring and non-destructive testing, little research has been conducted to establish its sources, particularly in 2024-T3 aluminium alloys. The major contribution of this work is that it provides a method to obtain a better linear relationship of count rate with crack growth rate based on waveform. This paper aims to characterise AE sources by synchronising the AE waveforms with load levels and then to propose possible dominant frequency ranges. The AE waveforms during fatigue crack growth in edge-notched 2024-T3 aluminium specimens, from an initial crack length of 10 mm to 70 mm, were collected at two different load ratios R = 0.125 and 0.5. At the same time, the crack growth rate was determined using thermal imaging and associated control software. The AE waveforms obtained were processed using the fast Fourier transform. It was shown that a significantly higher AE count rate was recorded at R = 0.125 compared to R = 0.5 when the maximum load was kept the same. This means that the R-ratio would affect the total amount of AE activities collected. It was also found that the dominant frequency range of the AE waveforms directly related to crack growth was 152–487 kHz, and the ranges due to crack closure were likely to be 310 kHz–316 kHz and 500–700 kHz. Based on the proposed frequency ranges, waveform selection was conducted and a better linear relationship between count rate and crack growth rate was observed. This study provides a better understanding of the AE sources and waveforms for future structural health monitoring applications.

Diabetic nephropathy (DN) is the main cause of end stage renal disease (ESRD). Glomerulus damage is one of the primary pathological changes in DN. To reveal the gene expression alteration in the glomerulus involved in DN development, we screened the Gene Expression Omnibus (GEO) database up to December 2020. Eleven gene expression datasets about gene expression of the human DN glomerulus and its control were downloaded for further bioinformatics analysis. By using R language, all expression data were extracted and were further cross-platform normalized by Shambhala. Differentially expressed genes (DEGs) were identified by Student's t-test coupled with false discovery rate (FDR) (P < 0.05) and fold change (FC) ≥1.5. DEGs were further analyzed by the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to enrich the Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. We further constructed a protein-protein interaction (PPI) network of DEGs to identify the core genes. We used digital cytometry software CIBERSORTx to analyze the infiltration of immune cells in DN. A total of 578 genes were identified as DEGs in this study. Thirteen were identified as core genes, in which LYZ, LUM, and THBS2 were seldom linked with DN. Based on the result of GO, KEGG enrichment, and CIBERSORTx immune cells infiltration analysis, we hypothesize that positive feedback may form among the glomerulus, platelets, and immune cells. This vicious cycle may damage the glomerulus persistently even after the initial high glucose damage was removed. Studying the genes and pathway reported in this study may shed light on new knowledge of DN pathogenesis.

Composite laminates have complex failure modes. In order to investigate the evolution of failure in the composite laminates, this paper performed an experimental study on four laminates with different layups using acoustic emission (AE) technique. Two different kinds of defects are imposed on the laminates, including a hole and a crack in the center. Tensile and bending tests are performed on the defective laminates and real-time AE signals are collected. By analyzing the spectrograms of the obtained AE signals and integrating with the dispersion curves, the evolution of failure modes for different laminates can be observed. The tests show that the defects cause multiple failure modes, which change gradually during the experiments. It is also revealed that laminates with different layups have different failure modes. More specifically, the stacking order of different plies has a greater impact on the occurrence of delamination and fiber fracture than matrix crack. The tentative research shows that there is great potential for improving the performance of the composite laminates by careful selection of ply layups.

Medium and small-scale high-clearance sprayers are widely applied in medium and small-scale farms. Owing to power and load limitations, it is difficult to manage the complex system for suppressing spray boom vibration. This study was conducted to design a spray boom-air suspension system suitable for medium and small-size high-clearance sprayers by combining spray boom vibration suppression and the characteristics of air spring charging/discharging. Thus, this study aims to address the non-homogeneous distribution of spray triggered by the spray boom vibrations in medium and small high-clearance sprayers. The effects of different elastic elements on the vibration suppression effect of the spray boom were compared. According to the bench test, the dynamic response results of the spray boom under transient and sinusoidal excitations indicate that air spring is more conducive to vibration suppression than coil spring. The results obtained from the field experiments indicate that under the low solid soil condition, the spray boom air suspension should match a small additional air chamber with a volume of approximately 0.6 L, and the damping coefficient of the damper should be approximately 1792 N·s/m. In the case of the high firm soil, the spray boom air suspension should match a large additional air chamber with a volume of approximately 3.6 L, while the damping coefficient of the damper should be set to approximately 1316 N·s/m. The soil with low moisture content and high firmness are unfavorable to the vibration suppression of the spray boom. This study provides a reference for enhancing the vibration suppression of the spray boom-air suspension and improving the spray uniformity of the sprayer.

RuO2 thin films were prepared using magnetron sputtering under different deposition conditions, including direct current (DC) and radio frequency (RF) discharges, metallic/oxide cathodes, different substrate temperatures, pressures, and deposition times. The surface morphology, residual stress, composition, crystal structure, mechanical properties, and pH performances of these RuO2 thin films were investigated. The RuO2 thin films RF sputtered from a metallic cathode at 250 °C exhibited good pH sensitivity of 56.35 mV/pH. However, these films were rougher, less dense, and relatively softer. However, the DC sputtered RuO2 thin film prepared from an oxide cathode at 250 °C exhibited a pH sensitivity of 57.37 mV/pH with a smoother surface, denser microstructure and higher hardness. The thin film RF sputtered from the metallic cathode exhibited better pH response than those RF sputtered from the oxide cathode due to the higher percentage of the RuO3 phase present in this film.

The mammalian hippocampus shows marked decline in function with aging across many species, including humans and laboratory rodent models. This decline frequently manifests in memory impairments that occur even in the absence of dementia pathology. In humans, a number of factors correlate with preserved hippocampal memory in aging, such as exercise, cognitive stimulation and number of social ties. While interventional studies and animal models clearly indicate that exercise and cognitive stimulation lead to hippocampal preservation, there is relatively little research on whether a decline in social ties leads to cognitive decline or vice versa. Even in animal studies of environmental enrichment in aging, the focus typically falls on physical enrichment such as a rotating cast of toys, rather than the role of social interactions. The present studies investigated the hypothesis that a greater number of social ties in aging mice would lead to improved hippocampal function. Aged, female C57/Bl6 mice were housed for 3 months in pairs or large groups (7 mice per cage). Group-housed mice showed greater novel object location memory and stronger preference for a spatial navigation strategy in the Barnes maze, though no difference in escape latency, compared to pair-housed mice. Group-housed mice did not differ from pair-housed mice in basal corticosterone levels or adult hippocampal neurogenesis. Group-housed mice did, however, show reduced numbers of Iba1/CD68+ microglia in the hippocampus. These findings suggest that group housing led to better memory function and reduced markers of neuroinflammation in aged mice. More broadly, they support a causative link between social ties and hippocampal function, suggesting that merely having a larger social network can positively influence the aging brain. Future research should address the molecular mechanisms by which a greater number of social ties alters hippocampal function.

Escherichia coli O157:H7 is an important food-borne pathogen that can cause hemorrhagic colitis and hemolytic-uremic syndrome in humans. pO157_Sal, a novel conjugative plasmid is present in a Chinese O157:H7 outbreak strain Xuzhou21. Here we investigated the phenotypic and transcriptional differences between the wild type strain Xuzhou21 and the pO157_Sal cured mutant strain Xuzhou21m. RNA-Seq analysis found that all 52 ORFs encoded on pO157_Sal were transcribed. One hundred and sixty eight chromosomal and pO157 genes were differentially expressed (≥2 fold difference) between Xuzhou21 and Xuzhou21m. Sixty-seven and 101 genes were up-regulated and down-regulated respectively by pO157_Sal including genes related to stress response, adaption and virulence. The plasmid-cured mutant Xuzhou21m grew slower than wild type Xuzhou21 and pO157_Sal plasmid complemented strain Xuzhou21c in M9 medium under the condition of high NaCl or presence of sodium deoxycholate (NaDC), corroborating with the RNA-Seq data. Seven differentially expressed genes are associated with NaDC resistance, including the adenine-specific DNA-methyltransferase gene (dam), multidrug efflux system subunit gene mdtA, hyperosmotically inducible periplasmic protein gene osmY and oxidation-reduction related genes while two differentially expressed genes (osmY and pspD) are likely to be related to resistance to osmotic pressure. A number of differentially expressed genes were virulence associated including four genes encoding T3SS effectors from the chromosome and ehxD from pO157. Through complementation of Xuzhou21m with a plasmid construct carrying the pO157_Sal hha homolog we further showed that the pO157_Sal hha represses the expression of T3SS effectors. These findings demonstrated that the plasmid pO157_Sal affects the transcription of the chromosomal and pO157 plasmid genes and contributes to the enhanced ability to resist stress. We conclude that pO157_Sal plays an important role in regulating global gene expression and affects the virulence and adaptation of E. coli O157:H7.

The mammalian hippocampus shows marked decline in function with aging across many species, including humans and laboratory rodent models. This decline frequently manifests in memory impairments that occur even in the absence of dementia pathology. In humans, a number of factors correlate with preserved hippocampal memory in aging, such as exercise, cognitive stimulation and number of social ties. While interventional studies and animal models clearly indicate that exercise and cognitive stimulation lead to hippocampal preservation, there is relatively little research on whether a decline in social ties leads to cognitive decline or vice versa. Even in animal studies of environmental enrichment in aging, the focus typically falls on physical enrichment such as a rotating cast of toys, rather than the role of social interactions. The present studies investigated the hypothesis that a greater number of social ties in aging mice would lead to improved hippocampal function. Aged, female C57/Bl6 mice were housed for 3 months in pairs or large groups (7 mice per cage). Group-housed mice showed greater novel object location memory and stronger preference for a spatial navigation strategy in the Barnes maze, though no difference in escape latency, compared to pair-housed mice. Group-housed mice did not differ from pair-housed mice in basal corticosterone levels or adult hippocampal neurogenesis. Group-housed mice did, however, show reduced numbers of Iba1/CD68+ microglia in the hippocampus. These findings suggest that group housing led to better memory function and reduced markers of neuroinflammation in aged mice. More broadly, they support a causative link between social ties and hippocampal function, suggesting that merely having a larger social network can positively influence the aging brain. Future research should address the molecular mechanisms by which a greater number of social ties alters hippocampal function. [ABSTRACT FROM AUTHOR]

Existing second language acquisition research converges on a picture where learners of English exhibit marked divergence from native speakers in their use of information-packaging constructions, even at advanced stages of acquisition. This study extends the investigation of these constructions to an emerging institutionalised second language variety, Hong Kong English. Based on the Hong Kong and British components of the International Corpus of English, the study examines the formal and functional properties of it-clefts and wh-clefts, revealing regional variation in a number of areas, particularly in the use of that's why constructions. Importantly, the grammar of the contact variety is found to be shaped by the transfer of gradient grammatical rules from the substrate language, and by stratification along stylistic parameters. [ABSTRACT FROM AUTHOR]

This paper deals with the "hot news" use of the English present perfect. Previous research has suggested that this use marks the end point of the perfect category, paving the way for further grammaticalisation to a perfective or past tense. To examine its historical development in Modern English, verb forms in the leads of hard news reports in the New York Times and the Sydney Morning Herald were examined, with comparison made between two time periods, 1851-1900 and 1951-2000. Attention was given to contextual influence on the choice between the present perfect and the past tense for expressing hot news meanings. The quantitative findings show that the hot news perfect has not taken over the ground of other tense forms, but has become increasingly associated with unspecified, recent past time. The evolution of the English present perfect in general is characterised by register-mediated functional specialisation. [ABSTRACT FROM AUTHOR]

Background: Whole-genome sequencing is an important method to understand the genetic information, gene function, biological characteristics and survival mechanisms of organisms. Sequencing large genomes is very simple at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. Shotgun sequencing method failed to complete the sequence of this genome. Results: After persevering for 10 years and going over three generations of sequencing techniques, we successfully completed the sequence of the PaP1 genome with a length of 91,715 bp. Single-molecule real-time sequencing results revealed that this genome contains 51 N-6-methyladenines and 152 N-4-methylcytosines. Three significant modified sequence motifs were predicted, but not all of the sites found in the genome were methylated in these motifs. Further investigations revealed a novel immune mechanism of bacteria, in which host bacteria can recognise and repel modified bases containing inserts in a large scale. This mechanism could be accounted for the failure of the shotgun method in PaP1 genome sequencing. This problem was resolved using the nfi− mutant of Escherichia coli DH5α as a host bacterium to construct a shotgun library. Conclusions: This work provided insights into the hard-to-sequence phage PaP1 genome and discovered a new mechanism of bacterial immunity. The methylome of phage PaP1 is responsible for the failure of shotgun sequencing and for bacterial immunity mediated by enzyme Endo V activity; this methylome also provides a valuable resource for future studies on PaP1 genome replication and modification, as well as on gene regulation and host interaction. [ABSTRACT FROM AUTHOR]

Bacteria develop a broad range of phage resistance mechanisms, such as prevention of phage adsorption and CRISPR/Cas system, to survive phage predation. In this study, Pseudomonas aeruginosa PA1 strain was infected with lytic phage PaP1, and phage-resistant mutants were selected. A high percentage (∼30%) of these mutants displayed red pigmentation phenotype (Red mutant). Through comparative genomic analysis, one Red mutant PA1r was found to have a 219.6 kb genomic fragment deletion, which contains two key genes hmgA and galU related to the observed phenotypes. Deletion of hmgA resulted in the accumulation of a red compound homogentisic acid; while A galU mutant is devoid of O-antigen, which is required for phage adsorption. Intriguingly, while the loss of galU conferred phage resistance, it significantly attenuated PA1r in a mouse infection experiment. Our study revealed a novel phage resistance mechanism via chromosomal DNA deletion in P. aeruginosa. [ABSTRACT FROM AUTHOR]

Background: Streptococcus suis serotype 2 (S. suis 2) has evolved efficient mechanisms to cause streptococcal toxic shock syndrome (STSS), which is a new emerging infectious disease linked to S. suis. We have previously reported that a type IV secretion system (T4SS) harbored by the specific 89K pathogenicity island (PAI) of S. suis 2 contributes to the development of STSS and mediates horizontal transfer of 89K. However, the 89K T4SS machinery assembly in vivo and in vitro is poorly understood, and the component acting directly to digest the bacterial cell wall needs to be identified. Results: The virB1-89K gene product encoded in the 89K PAI is the only one that shows similarity to the Agrobacterium VirB1 component and contains a conserved CHAP domain that may function in peptidoglycan hydrolysis, which makes it a plausible candidate acting as a hydrolase against the peptidoglycan cell wall to allow the assembly of the T4SS apparatus. In the current study, the CHAP domain of VirB1-89K from S. suis 89K PAI was cloned and over-expressed in Escherichia coli, and its peptidoglycan-degrading activity in vitro was determined. The results indicated that the VirB1-89K CHAP domain can degrade the peptidoglycan layer of bacteria. Deletion of virB1-89K reduces significantly, but does not abolish, the virulence of S. suis in a mouse model. Conclusions: The experimental results presented here suggested that VirB1-89K facilitates the assembly of 89K T4SS apparatus by catalyzing the degradation of the peptidoglycan cell wall, thus contributing to the pathogenesis of S. suis 2 infection. [ABSTRACT FROM AUTHOR]

A number of recent studies of grammatical categories in English have identified regional and diachronic variation in the use of the present perfect, suggesting that it has been losing ground to the simple past tense from the eighteenth century onwards (Elsness, 1997, 2009; Hundt and Smith, 2009; and Yao and Collins, 2012). Only a limited amount of research has been conducted on «on-present perfects. More recently, Bowie and Aarts' (2012) study using the Diachronic Corpus of Present-Day Spoken English has found that certain non-present perfects underwent a considerable decline in spoken British English (BrE) during the second half of the twentieth century. However, comparison with American English (AmE) and across various genres has not been made. This study focusses on the changes in the distribution of four types of non-present perfects (past, modal, ro-infinitival and /«g-participial) in standard written BrE and AmE during the thirty-year period from the early 1960s to the early 1990s. Using a tagged and post-edited version of the Brown family of corpora, it shows that contemporary BrE has a stronger preference for non-present perfects than AmE. Comparison of four written genres of the same period reveals that, for BrE, only the change in the overall frequency of past perfects was statistically significant. AmE showed, comparatively, a more dramatic decrease, particularly in the frequencies of past and modal perfects. It is suggested that the decline of past perfects is attributable to a growing disfavour for past-time reference in various genres, which is related to long-term historical shifts associated with the underlying communicative functions of the genres. The decline of modal perfects, on the other hand, is more likely to be occurring under the influence of the general decline of modal auxiliaries in English. [ABSTRACT FROM AUTHOR]

This article reports findings from a comprehensive corpus-based study of several verbal categories in Malaysian English: modals/quasi-modals, progressives and present perfects. Comparisons are drawn with a further five varieties of World English: two Inner Circle and three Outer Circle. For the verbal categories selected there is independent evidence of recent diachronic variation in British English and American English. Apparent time insights into the degrees of advancement of Malaysian English and the Outer Circle Englishes with respect to these changes are derived via comparisons of speech versus writing frequencies, and comparisons with frequencies for the Inner Circle varieties. The findings suggest that Malaysian English is exonormatively oriented toward the current global English superpower, American English, and that there is a continuing reluctance to accept colloquial grammatical features in more formal registers of Malaysian English. [ABSTRACT FROM AUTHOR]

Background and purpose: The occurrence of lymph node metastasis in papillary thyroid cancer (PTC) can have adverse effects on the prognosis of patients. This study aimed to investigate risk factors related to the occurrence of contralateral central lymph node metastases (CLNM) and contralateral lateral lymph node metastases (LLNM) when imaging suspected ipsilateral LLNM in unilateral PTC. Methods: We retrospectively analyzed the clinical data of 526 patients who received surgical treatment in the same treatment group of Jiangsu Cancer Hospital Head and Neck Surgery Department from January 2011 to December 2021. They were initially treated with total thyroidectomy and bilateral central lymph node dissection (CLND) ± lateral lymph node dissection, and their postoperative pathology was uni-PTC. This study analyzed the relevant high-risk factors of contralateral lymph node metastasis. Results: Among the 526 patients, 295 had CLNM, including 272 ipsilateral CLNM, 129 contralateral CLNM and 106 of both sides CLNM; 165 patients had LLNM including 129 ipsilateral LLNM, 18 contralateral LLNM, and 18 of both ipsilateral and contralateral LLNM. Contralateral CLNM occurred in 65 (17.8%) of 365 patients who underwent preventive CLND, and contralateral CLNM was found in 68 (42.2%) of 161 patients with therapeutic CLND. Univariate and multivariate regression analyses showed that contralateral CLNM was associated with maximum diameter of tumor ≥2 cm, multiple foci, no Hashimoto's thyroiditis, tumor invasion, number of CLNM≥6 and age